Molecular structures and crystal packings of 2-styrylquinoline and its derivatives

The crystal and molecular structures of five styrylheterocycles of the quinoline series are studied. All molecules are planar. The double bond in the ethylene fragment is essentially localized. In the molecule of 2-(4-methylstyryl)quinoline, the ethylene fragment is disordered by the bicycle-pedal pattern. In four of the five compounds, the crystal packings do not contain stacking dimers prearranged for the [2+2] photocycloaddition (PCA) reaction. In the crystal of 2-(3-nitrostyryl)quinoline, pairs of crystallographically independent molecules form stacking dimers. In a dimer, the ethylene fragments have a twist orientation, which is incompatible with the PCA reaction. An attempt to initiate a temperature-dependent process of bicyclepedal isomerization in the crystal and, as a consequence, the PCA reaction by means of simultaneous irradiation and heating of a single crystal is unsuccessful.     

Specific features of the crystal packing that enable styryl dyes of the pyridine series to undergo the solid-phase [2 + 2] photocycloaddition including the process with single crystal retention

The crystal packing of a number of styryl dyes of the pyridine series is analyzed. The structures of three dyes and three [2 + 2] photocycloaddition (PCA) products, 1,2,3,4-tetrasubstituted cyclobutanes, obtained in single crystals are determined by X-ray diffraction. Stacks of planar organic cations are characteristic of styryl dye packings. The proceeding of the PCA reaction as a single crystal-to-single crystal transformation in the syn head-to-head stacks is in principle impossible. The syn head-to-tail stacking packings are favorable for the PCA reactions resulting in the centrosymmetric rctt isomers of cyclobutane. The stacking packings, in which molecules are related by the twofold axes (the anti arrangement of molecules), are also favorable for PCA in single crystals. In this case, the products are the rtct isomers of cyclobutane. The presence of the I^? counterions in a packing is a factor impeding the PCA reaction, because the secondary I…H-C bonds increase the rigidity of the crystal lattice. The conditions necessary for proceeding the PCA reactions in styryl dyes as single crystal-to-single crystal processes are as follows: (1) the stacks split into pairs of organic cations (dimers) with the d distances within 4.2 Å in a dimer and d exceeding 4.2 Å between the dimers; and (2) the dimers are surrounded by flexible shells consisting of anions, solvate molecules, or flexible moieties of the organic cations themselves.     

Crystal and molecular structure of a series of 15-crown-5-containing styryl heterocycles and their dimethoxy substituted analogues

A comparative study of the molecular geometry and crystal packing of crown-containing styryl heterocycles and their dimethoxy substituted analogues is performed. It is established that all the compounds exhibit an identical type of distortions of the geometry of the central styryl fragment. These are the localization of the π-electron density at the ethylene bond and the bond alternation in a half of the phenyl ring due to the conjugation of lone electron pairs of the oxygen substituents with the chromophore system of the molecule. A comparative analysis of the crystal packings of the compounds reveals extended separate hydrophilic and hydrophobic regions. The hydrophilic regions are built of crown ether fragments, and the hydrophobic regions consist of π-conjugated and aromatic molecular fragments. The hydrophobic regions are characterized by a wide variety of packing motifs, among which stacking packing is absent. For two compounds, the formation of sandwich dimers that are preorganized to enter into the photochemical [2 + 2]cycloaddition reaction is observed.     

3-叔丁基-1-(3-羟基苯基)脲的晶体结构及密度泛函理论研究

脲类及其衍生物在化学、农业、医学等多个领域有重要用途。而芳基脲类化合物是一类重要的医药化工中间体,本文经酰化和氧化两步反应制备3-叔丁基-1-(3-羟基苯基)脲,并于室温下经溶剂挥发法获得其单晶体,对晶体的堆积及分子间作用模式进行了分析。其结构经核磁共振氢谱(¹H NMR)、红外光谱(FT-IR)、核磁共振碳谱(¹³C NMR)、质谱MS和X射线单晶衍射等方法确证,在B3LYP/6-311+G(2d, p)模式下使用密度泛函理论(DFT)进行了最优结构以及前沿轨道能量计算,对比了晶体与理论计算的分子结构。结果表明,经DFT优化的分子结构与X-射线单晶衍射确定的晶体结构基本一致,该化合物为单斜方P2₁/n空间群,晶胞参数为a=1.181 42(6) nm,b=1.762 00(8) nm,c=1.179 02(5) nm,Z=8。     

Synthesis and crystal structure of α,β-unsaturated ketone: 3,3′-[1,2-ethanediylbis(oxy-2,1-phenylene)]bis[1-(2-pyridyl)-2-propen-1-one]

The title compound, C₃₀H₂₄N₂O₄, 3,3′-[1,2-ethanediyl-bis(oxy-2,1-phenylene)]bis[1-(2-pyridyl)-2-propen-1-one] was synthesized and characterized by elemental analysis, FT-IR spectra, ¹H NMR, and X-ray single-crystal diffraction. In the molecule, the pyridine plane and the adjacent phenyl plane are almost coplanar with the dihedral angle of 3.07°, while the dihedral angle between the mean planes of the two asymmetric units is 67.56°. The crystal packing is stabilized by weak intermolecular C-H...N and C-H...O hydrogen bonds, C-H...π and π...π stacking interactions.     

X-ray diffraction study of p -(alkoxybenzylidene)- p ′-toluidines C5H11O-C6H4-CH=N-C6H4-CH3 and C8H17O-C6H4-CH=N-C6H4-CH3

The molecular and crystal structures of two p-(alkoxybenzylidene)-p′-toluidines C₅H₁₁O-C₆H₄-CH=N-C₆H₄-CH₃ (1) and C₈H₁₇O-C₆H₄-CH=N-C₆H₄-CH₃ (2), which form the nematic phase upon melting, is determined by X-ray diffraction. The geometry of the benzylideneaniline fragments in molecules 1 and 2 is actually identical. The crystal packings of 1 and 2 are characterized by the alternation of layers formed by loosely packed aliphatic fragments of molecules and layers of closely packed aromatic fragments. The packing in the aromatic regions of 1 follows the parquet pattern. The crystal packing of 2 has a stacking structure, which is formed by π-stacking dimers superimposed on one another. The formation of the mesogenic phase upon melting of crystals 1 is due to the disturbance of the structurality of loose aliphatic layers with retention of the structure of the aromatic regions, which are stabilized by the cooperative effect of weak directed C-H ··· π-system interactions. The mesogenic phase of crystals 2 is formed upon melting as a consequence of the retention of the structure of π-stacking dimers. Original Russian Text ? L.G. Kuz’mina, N.S. Kucherepa, M.N. Rodnikova, 2008, published in Kristallografiya, 2008, Vol. 53, No. 6, pp. 1079–1085.     

Syntheses and Crystal Structures of Two Apigenin Alkylation Derivatives

Abstract Two apigenin alkylation derivatives, 4′,7-dimethoxyl-5-hydroxyflavone (I) and 4′,7-diethoxyl-5-hydroxyflavone (II), have been synthesized and their crystal structures were determined by ¹H NMR and single crystal X-ray diffraction study. (I) is triclinic, space group P−1 with a = 7.120(5) ?, b = 7.297(5) ?, c = 13.559(10) ?, α = 89.313(12)°, β = 86.298(12)°, γ = 83.999(13)° and Z = 2. (II) is monoclinic, space group P 2₁ /c with a = 16. 309(4) ?, b = 7.303(2) ?, c = 15.185(4) ?, α = 90.00°, β = 115.70(2)°, γ = 90.00° and Z = 4. They have the same flavone skeleton which is composed of a benzopyranone moiety and a phenyl moiety. Molecules of (I) are linked into a two-dimensional network by a combination of C–H···O hydrogen bond and π–π stacking interactions. (II) shows some discrepancies with (I) and the molecules are linked into a column by π–π stacking interaction. Graphical Abstract Two apigenin alkylation derivatives, 4′,7-dimethoxyl-5-hydroxyflavone (I) and 4′,7-diethoxyl-5-hydroxyflavone (II) were synthesized and their crystal structures were determined by single-crystal X-ray diffraction. Hydrogen bonding and π–π stacking interactions assemble (I) into a two-dimensional network, and in the crystal structure of (II), π–π stacking interaction leads to the formation of a column.      

X-ray crystal structural analysis of 1,2-dihydro-3-methylpyrazole-5-one

The title compound 1,2-dihydro-3-methylpyrazole-5-one was determined by X-ray crystal structural analysis. The crystals are monoclinic, with space group P2(1)/n with a = 7.968(7), b = 6.502(6), c = 9.986(10) Å, α = 90°, β = 109.995(15)°, γ = 90°, V = 486.1(8) ų, Z = 4, F(000) = 208, D_c = 1.340 g cm^–3, μ = 0.100 mm^?1, and the final R = 0.0373 and wR = 0.0961. A total of 4776 reflections were collected, of which 1148 were independent (R_int = 0.0589). In the crystal packing diagram, intermolecular N?H···O hydrogen bonds and π?π stacking interactions stabilize the solid state of the title compound.     

A Novel Supramolecular Complex Based on Zaltoprofen Ligand: Synthesis,Crystal Structure,and Properties

A novel metal-organic supramolecular complex [Zn₂ (Zaltoprofen)₂(phen)₂] (where Zaltoprofen = 5-(1-carboxyethyl)-2-(phenylthio)phenylacetic acid, phen = 1,10-phenanthroline) has been synthesized under hydrothermal condition and characterized by single crystal X-ray diffraction, elemental analysis, spectral method (IR), powder X-ray diffraction (XRD), electronic Spectra (UV-vis), and fluorescent properties. The compound crystallizes in the monoclinic P2(1)/c space group. [Zn₂(Zaltoprofen)₂(phen)₂] features 0-D structural, the π–π stacking interactions and C?H···O hydrogen-bonds play a vital role in determining the crystal packing and construction of the extended 3-D supramolecular network.     

Crystal Structure of 2‐methyl cinnamanilide and 2‐methoxy cinnamanilide

The crystal structures of two cinnamanilide derivatives 2‐methyl cinnamanilide (C₁₆ H₁₅ N O – compound I) and 2‐methoxy cinnamanilide (C₁₆ H₁₅ N O₂ – compound II) are reported. In both crystal structures, the cinnamamide group is almost planar. The inter‐planar angle between the two phenyl rings are 71.6(1)° for compound I and 7.5(1)° for compound II. The N‐H…O and C‐H…O type of hydrogen bond interactions between the amide group and the carbonyl group stabilizes the molecular packing as chains in the crystal lattice.     

Structural regularities of helicoidally-like biopolymers in the framework of algebraic topology: II. α-Helix and DNA structures

The developed apparatus of the “structural application” of algebraic geometry and topology makes it possible to determine topologically stable helicoidally-like packings of polyhedra (clusters). A packing found is limited by a minimal surface with zero instability index; this surface is set by the Weierstrass representation and corresponds to the bifurcation point. The symmetries of the packings under consideration are determined by four-dimensional polyhedra (polytopes) from a closed sequence, which begins with diamondlike polytope {240}. One example of these packings is a packing of tetrahedra, which arises as a result of the multiplication of a peculiar starting aggregation of tetrahedra by a fractional 40/11 axis with an angle of helical rotation of 99°. The arrangement of atoms in particular positions of this starting aggregation allows one to obtain a model of the α-helix. This apparatus makes it possible to determine a priori the symmetry parameters of DNA double helices.     

Polyelectrolytes inhibition effect on crystallization of gypsum

The spontaneous precipitation of calcium sulfate dihydrate (gypsum) at 30 °C was investigated in the presence of polyelectrolytes. The degree of inhibition is measured as the reduction in initial crystallization rate, determined by conductivity of the crystallizing solution. The inhibition increases with acid content of the copolymer. Changing the butyl ester to a hydrophilic ethylene oxide resulted in higher inhibition efficiency. The inhibition efficiency is believed to arise from the closer chain packing on the crystal surface. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Synthesis,spectroscopic characterization and crystal structure of 5-bromo-1-(2-cyano-pyridin-4-yl)-1H-indazole-3-carboxylic acid diethylamide

The title compound 5-bromo-1-(2-cyano-pyridin-4-yl)-1H-indazole-3-carboxylic acid diethylamide, C₁₈H₁₆BrN₅O, is prepared from 5-bromoindazole-3-carboxylic acid methylester. N ¹-arylation is carried out with 4-chloro-2-cyanopyridine and the resulting product is converted to diethylamide by reacting with thionyl chloride and diethylamine. The structure is identified from its FT-IR, ¹H NMR, ¹³C NMR spectroscopy, elemental analysis data and unambiguously confirmed by single crystal X-ray diffraction studies. There are two symmetry independent molecules in the asymmetric unit with no significant differences in bond lengths and angles. The title compound crystallizes in the triclinic system, space group \(P\bar 1\) , with a = 11.2330(2); b = 11.6130(2); c = 15.4710(3) Å, α = 92.515(1)°; β = 109.956(1)°; γ = 107.199(1)°; V = 1788.45(6)ų and z = 4. An intramolecular C-H…N hydrogen bond forms an S(6) ring motif in one of the unique molecules. In the crystal, two molecules are linked about a center of inversion by C-H…O hydrogen bonded dimers generating an R ₂ ² (16) ring motif. The crystal packing is stabilized by C-H…N, C-H…O hydrogen bonds and π…π stacking interactions.     

Supramolecular structure of 5-methyl-5-phenyl hydantoin and hydrogen-bonding patterns in 5,5′-substituted hydantoins

The crystal structure of heterocyclic compound 5-methyl-5-phenyl hydantoin has been determined from X-ray single crystal structural characterization. This material crystallizes in the orthorhombic system and noncentrosymmetric space group P21 (N°4). The crystal packing is governed by N–H···O hydrogen bond-type intermolecular interactions, forming chains and edge-fused 12-membered rings with graph-set C(4) C(5) C22(8) R33(12) in a similar hydrogen-bonding pattern of another chiral 5,5′-substituted hydantoins.     

PM3 semiempirical study and its comparison with X-ray crystal structure of 4-[2-Methyl-4-(4-methoxyphenylazo)] phenoxyphtalonitrile

  The molecular and crystal structures of the title compound, C₂₂H₁₆N₄O₂, were determined by single crystal X-ray diffraction technique. The title compound crystallizes in monoclinic space group P1 2 ₁ /n1, with a=12.7811(9) ?, b=8.2002(4) ?, c=17.8772(14) ?, Z=4, D _calc=1.3112(1) g/cm³, μ (Mo-K_α)=0.087 mm⁻¹. The structure was solved by direct methods and refined to a final R=0.056 for 1891 reflections with I > 2σ (I). The asymmetric unit in the crystal structure contains only one neutral molecule. The positions of nitrogen atoms in the azo groups were disordered. There is no classic hydrogen bond in the crystal structure. The molecules in the crystal structure are stacked by π–π stacking and one edge-to-face interactions. In order to determine conformational flexibility and crystal packing effects on the molecules, molecular energy profile of the title compound was obtained with respect to the selected torsion angle, which is varied from −180° to +180° in every 10° via PM3 semi-empirical method.     

Co-crystal structure and optical properties of 9-fluorenone and naphthalene-1, 5-diamine

The co-crystal of 9-fluorenone and naphthalene-1, 5-diamine has been prepared and its structure is characterized by single-crystal X-ray analysis. It belongs to monoclinic system, space group P2₁/c with a = 9.0421(7), b = 18.1114(14), c = 8.1444(6) Å; β = 104.7232(10)°; V = 1296.20(17) ų, Z = 4. The crystal packing is stabilized by N-H…O intermolecular hydrogen bonds, as well as π-π stacking. Optical studies showed that the co-crystal exhibited red shift in PMMA film. The hydrogen bonds were easily destroyed in solvent.     

The Crystal Structures of O,O‐Dimethylalpinumisoflavone and 5‐O‐Methyl‐4'‐O‐(3‐methyl‐but‐2‐en‐1‐yl)alpinumisoflavone

The petrol extract of the rootbark of Milletia Thonningii obtained by column chromatography afforded sixteen different crystalline samples to be isolated. The crystal structures of two of these compounds, O,O‐Dimethylalpinumisoflavone (I) and 5‐O‐Methyl‐4'‐O‐(3‐methyl‐but‐2‐en‐1‐yl)alpinumisoflavone (II) are being reported here. (II) has two independent molecules in the asymmetric unit and differs from (I) in a longer side chain attached to C(15) of the phenyl ring. The structural features of the three molecules in the title compounds are reported and compared. The derivatives, being subject of this article are the first reported crystal structures where the isoflavone fragment is fused to a further six membered ring that results in a tricyclic ring system. The benzopyrone fragments are planar. The dihedral angles between the benzopyrone fragment and the phenyl ring being 55.38(6)° for (I) and 44.75(15)° /44.64(15)° for the respective independent molecules of (II) are within the range of values observed for similar structures.     

Molecular and crystal structures of calix[4]arene 1,3-di-<Emphasis Type="Italic">n</Emphasis>-propyl ether

The molecular and crystal structures of calix[4]arene 1,3-di-n-propyl ether are determined. The molecule adopts a cone conformation stabilized by a pair of hydrogen bonds of the O-H?OR type (R is n-propyl). The dihedral angles between the planes of the benzene rings and the plane passing through the oxygen atoms are equal to 35.0°, 68.5°, 39.8°, and 71.2°. The larger angles are characteristic of the rings consisting of the ether groups, whereas the smaller angles are observed in the phenol rings. The bond lengths and angles in the molecule have standard values. In the crystal, the molecules form centrosymmetric dimers due to stacking interactions between two benzene rings in each dimer. Each of these rings is enclosed in the cavity of the other molecule in the dimer. The dimers have the shape of an ellipsoid. The packing as a whole can be described as an ellipsoid packing in which all the contacts occur through van der Waals interactions.     

Crystal structure of N,N ′-bis(cyclohexyl)-1-(N,N-dihexylamino)perylene-3,4:9,10-bis(dicarboximide)

An asymmetric dialkylamino-substituted perylene bisimide (1), N,N′-bis(cyclohexyl)-1-(N,N-dihexylamino)perylene-3,4:9,10-bis(dicarboximide), was synthesized and characterized by single-crystal X-ray diffraction. The crystal belongs to triclinic, space group P–1, with a = 9.8924(6), b = 14.6338(10), c = 15.6221(10) Å, α= 105.098(3)°, β = 103.386(2)°, γ = 107.772(3)°, and Z = 2. The central perylene core of 1 is twisted with dihedral angles of 14.9(3)° and 11.6(3)°; this twist configuration induces the axial chirality in this family of perylene bisimide dyes. In the crystal structure, the intermolecular C–H···O interaction links a pair of molecules into a cyclic centrosymmetric dimer that is connected to one another via the intermolecular π–π stacking, so linking the molecules into a continuous one-dimensional framework along the [100] direction.     

Spectral and X-ray Diffraction Studies of <Emphasis Type="Italic">N</Emphasis>-(2-Nitrophenyl)-5-Phenyl-1,3,4-Oxadiazole-2-Amine

Abstract  

Thiosemicarbazides and their derivatives are well known for their use in biological activity and many applications in pharmaceutical and industrial fields. The cyclization of 1-benzoyl-4-(2-nitrophenyl)-3-thiosemicarbazide (BNPTSC) in dimethylformamide (DMF) medium furnished N-(2-nitrophenyl)-5-phenyl-1,3,4-oxadiazole-2-amine (NPPOA). The chemical structure of the above substituted 1,3,4-oxadiazole has been assigned by IR, mass and X-ray diffraction studies. The XRD studies reveal the presence of four types of hydrogen bonds (N–H···O, N–H···N, C–H···O, C–H···N) in the crystal packing. The crystal system was found to be orthorhombic with a space group Pca2(1) and the unit cell dimensions are: a = 26.873(3) ?, b = 6.0827(7) ?, c = 7.8502(10) ?, α = 90°, β = 90°, γ = 90° and Z = 4.